/Users/eway/.pyenv/versions/3.8.3/lib/python3.8/site-packages/pandas/compat/__init__.py:97: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.
  warnings.warn(msg)
/Users/eway/.pyenv/versions/3.8.3/lib/python3.8/site-packages/requests/__init__.py:89: RequestsDependencyWarning: urllib3 (1.26.7) or chardet (3.0.4) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported "

cam = OpenHSI()

Running in notebook slow downs.

To add a custom camera, five methods need to be defined in a class to:

Initialise camera __init__,
Open camera start_cam,
Close camera stop_cam, and
Capture a picture as a numpy array get_img.
Update the exposure settings set_exposure

By inheriting from the OpenHSI class, all the methods to load settings/calibration files, collect datacube, saving data to NetCDF, and viewing as RGB are integrated. Furthermore, the custom camera class can be passed to a SettingsBuilder class for calibration.

with SimulatedCamera(img_path="assets/great_hall_slide.png", n_lines=1028, processing_lvl = 3, json_path="assets/cam_settings.json",pkl_path="assets/cam_calibration.pkl") as cam:
    cam.collect()
    fig = cam.show(hist_eq=True)
    
fig

100%|██████████| 1028/1028 [00:17<00:00, 58.00it/s]

plt.imshow(cam.rgb_buff.data)

<matplotlib.image.AxesImage at 0x125f75340>

plt.plot(cam.λs,cam.xs[0],'r',label="X(λ)")
plt.plot(cam.λs,cam.ys[0],'g',label="Y(λ)")
plt.plot(cam.λs,cam.zs[0],'b',label="Z(λ)")
plt.grid(); plt.minorticks_on()
plt.legend()
plt.xlabel("λ (nm)")
plt.ylabel("CIE XYZ value")

plt.plot(cam.binned_wavelengths,cam.dc.data[350,300,:],label="rock")
plt.plot(cam.binned_wavelengths,cam.dc.data[50,300,:], label="sky")
plt.plot(cam.binned_wavelengths,cam.dc.data[150,300,:],label="water")
plt.legend()
plt.xlabel("wavelength (nm)")
plt.ylabel("pseudo-spectra")

Below is still experimental stuff

with ProcessDatacube(fname = "../load_multiple/2021-05-26 03_26_26.011211.nc",n_lines=3072,processing_lvl=-1) as cam:
    cam.collect()
    fig = cam.show(robust=True)
    
fig

  0%|          | 0/3072 [00:00<?, ?it/s]

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-18-c433f48491e5> in <module>
      1 with ProcessDatacube(fname = "../load_multiple/2021-05-26 03_26_26.011211.nc",n_lines=3072,processing_lvl=-1) as cam:
----> 2     cam.collect()
      3     fig = cam.show(robust=True)
      4 
      5 fig

<ipython-input-8-b1e53126560f> in collect(self)
     23         self.start_cam()
     24         for i in tqdm(range(self.n_lines)):
---> 25             self.put(self.get_img())
     26 
     27             if callable(getattr(self,"get_temp",None)):

~/Desktop/openhsi/openhsi/data.py in put(self, x)
    376         """Applies the composed tranforms and writes the 2D array into the data cube. Stores a timestamp for each push."""
    377         self.timestamps.update()
--> 378         self.dc.put( self.pipeline(x) )
    379 
    380 

~/Desktop/openhsi/openhsi/data.py in put(self, line)
     73     def put(self, line:np.ndarray):
     74         """Writes a (n-1)darray into the buffer"""
---> 75         self.data[tuple(self.write_pos)] = line
     76 
     77         # if buffer full, update read position to keep track of oldest slot

ValueError: could not broadcast input array from shape (452,108) into shape (772,2064)

x = np.zeros((3, 4, 5))
x = np.moveaxis(x, -1, 0)
np.moveaxis(x, 0, -1).shape

(3, 4, 5)

`class` `OpenHSI`[source]

`OpenHSI.collect`[source]

`class` `SimulatedCamera`[source]

`class` `ProcessDatacube`[source]

class OpenHSI[source]

OpenHSI.collect[source]

class SimulatedCamera[source]

class ProcessDatacube[source]

`class` `OpenHSI`[source]

`OpenHSI.collect`[source]

`class` `SimulatedCamera`[source]

`class` `ProcessDatacube`[source]